Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.13 kDa 
• Atom Count: 3181 
• Modelled Residue Count: 397 
• Deposited Residue Count: 413 
• Unique protein chains: 2

1TDQ

Structural basis for the interactions between tenascins and the C-type lectin domains from lecticans: evidence for a cross-linking role for tenascins

• PDB DOI: 10.2210/pdb1TDQ/pdb

• Classification: extracellular matrix
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli, Homo sapiens
• Mutation(s): No 


• Deposited: 2004-05-24 Released: 2004-08-31 
• Deposition Author(s): Lundell, A., Olin, A.I., Moergelin, M., al-Karadaghi, S., Aspberg, A., Logan, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Literature

Structural basis for interactions between tenascins and lectican C-type lectin domains: evidence for a crosslinking role for tenascins

Lundell, A., Olin, A.I., Moergelin, M., al-Karadaghi, S., Aspberg, A., Logan, D.T.

(2004) Structure 12: 1495-1506

• PubMed: 15296743 
• DOI: 10.1016/j.str.2004.05.021
• Primary Citation of Related Structures:  
  1TDQ


• PubMed Abstract: 
  

The C-terminal G3 domains of lecticans mediate crosslinking to diverse extracellular matrix (ECM) proteins during ECM assembly, through their C-type lectin (CLD) subdomains. The structure of the rat aggrecan CLD in a Ca(2+)-dependent complex with fibronectin type III repeats 3-5 of rat tenascin-R provides detailed support for such crosslinking. The CLD loops bind Ca2+ like other CLDs, but no carbohydrate binding is observed or possible. This is thus the first example of a direct Ca(2+)-dependent protein-protein interaction of a CLD. Surprisingly, tenascin-R does not coordinate the Ca2+ ions directly. Electron microscopy confirms that full-length tenascin-R and tenascin-C crosslink hyaluronan-aggrecan complexes. The results are significant for the binding of all lectican CLDs to tenascin-R and tenascin-C. Comparison of the protein interaction surface with that of P-selectin in complex with the PGSL-1 peptide suggests that direct protein-protein interactions of Ca(2+)-binding CLDs may be more widespread than previously appreciated.

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Organizational Affiliation: 

Department of Molecular Biophysics, Lund University, Box 124, S-221 00 Lund, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tenascin-R	A	283	Rattus norvegicus	Mutation(s): 0  Gene Names: Tnr
UniProt
Find proteins for Q05546 (Rattus norvegicus) Explore Q05546  Go to UniProtKB:  Q05546

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Aggrecan core protein	B	130	Rattus norvegicus	Mutation(s): 0  Gene Names: Agc1, Agc, Acan
UniProt
Find proteins for P07897 (Rattus norvegicus) Explore P07897  Go to UniProtKB:  P07897

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth B], D [auth B], E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.234 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.52	α = 90
b = 86.42	β = 90
c = 57.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-05-24 
• Released Date: 2004-08-31 
Deposition Author(s): Lundell, A., Olin, A.I., Moergelin, M., al-Karadaghi, S., Aspberg, A., Logan, D.T.

Revision History  

• Version 1.0: 2004-08-31
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2018-03-07
  Changes: Data collection
• Version 1.4: 2021-03-31
  Changes: Database references, Derived calculations, Source and taxonomy